i have one query. that if we have a multi domain protein structure to
solve ,and we know about only one small domain of the protein for MR .
other domain structure is not known then how we can proceed.
is there any procedure to utilize phase from the solution with known
domain .
Well - first use pointless to see if there is any agreement between the
two data sets. You can input the unmerged scalepack output..
Use the option - find Laue group for each data set - it will suggest if
you should have point group 222 or just 2.
And then the option.
match index to reference a
An excellent reference to start with..
Eleanor
James Stroud wrote:
Whether probing the bulletin boards for advice or probing nature for
her structural secrets, the first thing to do is to ask a good
question. The best advice I can give is to be specific with your
queries and do a little home
This is difficult..
Do you want to keep the same spacegroup and cell, or just embed that map
in a large P1 cell and use it for molecular replacement searches?
Eleanor
Anita paula Testa salmazo wrote:
Dear All,
I have masked a map in coot and exported it. Now I'm trying to use SFall
to conver
Joe wrote:
Hi,
Recently we determined two structures of the same protein in complex with
different molecules. The protein contains two domains (called domain A and
B here). In the two structures, domain A and B have different arrangements
relative to each other, resulting different interaction
Dear Yuan,
Most likely your ARP/wARP settings are not sourced.
1. Quit CCP4i
2. Modify your ./cshrc (or .bashrc) so that it sources CCP4 first and
ARP/wARP then. Below is one example of .cshrc:
#
# Setup CCP4
source /Users/victor/xtal/ccp4/ccp4-6.0.2/include/ccp4.setup
#
# Setup ARP/wARP
sour
>The way Phenix.refine refines a model with a high twin fraction is
different >(proportionality rules) which can introduce model bias, so your
model should >be pretty close to the end product. I recommend refining your
structure as >well as you can without inputting the twin law until the very
end.
Dear all,
Please see the following advertisement for a postdoc position at EMBL,
Grenoble. Please respond to ulli.we...@embl.de.
Kind regards,
Natalie Zhao
CCP4 Group
--
Postdoctoral Fellowship in Structural Biology
EMBL site:
EMBL Grenoble
Commencing date:
January 2
Research Associate in X-ray protein crystallography of light induced reactions
Employer:Imperial College London
Website:http://www.imperial.ac.uk/mol...
Location:Exhibition Road, South Kensington, London, SW7 2AZ
Posted:October 21, 2009
Expires:January 04, 2010
Requisition number: NS2009160AB
S
Dear colleagues,
We are pleased to announce that OASIS version 4.0 is now available.
This version includes an improved SAD-phasing algorithm and a GUI for
controlling and monitoring Dual-space iteration processes, which
involve phasing, density-modification and model-building programs.
More detail
Dear colleagues,
Please forward this information to students in your institutes who might be
interested.
Get on target to a career in the biomedical sciences!*
* la Caixa/IRB Barcelona International PhD Programme fellowships *
IRB Barcelona is an independent, non-profit research institution
Dear CCP4 community,
We are still looking for candidates with experience in macromolecular
crystallography and beamline instrumentation for a permanent scientific
position opening on the PROXIMA 2 beamline at Synchrotron SOLEIL (see
below for more details).
Please note the the deadline
Dear All,
I need some suggestions regarding the SAD phasing using home source. What
the the most commonly used HA for SAD phasing for Cu anode.
All suggestions are welcome.
Thanks.
James
This should do:
cad hklin1 original.mtz hklin2 refined.mtz hklout Fp_phase.mtz << EOF_CAD
LABIN FILE 1 E1=DANO
LABIN FILE 2 E1=PHWT E2=FOM
END
EOF_CAD
fft hklin Fp_phase.mtz mapout anom_diff.map
Hi,
you can try it in PHENIX:
- phenix.refine outputs such map by default (if input data file contains
Fobs+ and Fobs-);
- you can use a Create Maps option from main PHENIX GUI.
Pavel.
On 10/26/09 11:10 AM, Sergii Buth wrote:
Hello everybody!
I am faced with a problem of calculating an ano
I have had success with Iodine, soak your crystal in your cryo + Potassium
Iodide
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
james09 pruza
Sent: Monday, October 26, 2009 2:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] SAD phasing at home source
Or you can try also substituting anomalous cations into the mix, such as CsI,
take multiple data sets, and do MIRAS:
NaCl
NaI
CsCl
CsI
One would then be able to subtract the various differences to find the HA's. Cs
has a pretty good anomalous signal at CuKa wavelength (~8 electrons).
Jacob
Another way can use Iodination of tyrosines. You can use N-Iodo succinamid on
existing crystals or on protein prior to crystallization.
Raz
Raz Zarivach, Ph.D.
Department of Life Sciences and the NIBN
Ben-Gurion University of the Negev
POB 6
Dear James,
A little bit more "old school" but you might also try Uranium, Samarium
and Gadolinium.
In principle, take a look what compounds you have in your HA box and
afterwards check anomalous signal for example at
http://skuld.bmsc.washington.edu/scatter/AS_form.html
Best regards,
Georg
Xe is also an excellent anomalous scatterer at Cu Ka wavelength. It is
particularly good for SIRAS phasing since Xe derivative is usually highly
isomorphous to the native crystals.
Hong
_
Hong Zhang, Ph.D.
Department of Biochemistry
University of Texas Southwestern Medical Ce
I've had a run of good luck with magic triangle
(5-amino-2,4,6-triiodoisophthalic acid or I3C). Its inexpensive if
you buy the powdered form and make it yourself. And you can
quickly tell if you have the correct structure solution because
the iodines are arranged in equilateral triangles appro
You can also get anomalous maps from Refmac, just input F+ and F- and ANOM
MAPO keyword. See
http://www.ccp4.ac.uk/dist/html/refmac5/bugs_and_features.html for more
information if needed.
Pavol
if the link between the domains is not part of the interface then perhaps
a good first approximation may be to "cut" the linker and then use a
program such as APBS to compute the binding energy..
> Hi,
>
> Recently we determined two structures of the same protein in complex with
> different molec
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